Background Patients with chronic kidney disease (CKD) have inability to maintain the normal levels of protein metabolism products, blood pressure and hematocrit. Periodontal disease involves an inflammatory destructive process. Identification of opportunistic viruses is extremely important as they are associated with co‐morbidities. The objective of this study was to analyse the presence of human herpesviruses in saliva and gingival crevicular fluid (GCF) from patients with CKD. Methods One hundred and thirty one individuals were divided depending on the stage of CKD: Group 1 (clearance of creatinine > 75 mL/min) patients with no renal disease (n = 24); Group 2 (clearance of creatinine of 11‐75 mL/min) patients with renal disease (n = 67); Group 3 (clearance of creatinine < 10 mL/min) patients on hemodialysis (n = 40). The parameters of periodontal disease were evaluated. The viral detection was assessed by PCR. Results considering the three groups, the prevalence of herpes simplex virus 1 (HSV‐1) were 9% in saliva and 5% in GCF; Epstein‐Barr virus 36% in saliva and 39% in GCF; human cytomegalovirus (HCMV) 11% in GCF; varicella zoster virus 6% in saliva and 3% in GCF; of human herpesvirus‐6 (HHV‐6) 6% in saliva and 2% in GCF; and HHV‐7 44% in saliva and 8% in GCF. Of these patients, 46.48% presented with severe periodontitis. A statistically significant association between HSV‐1 and HCMV was found in hemodialysis patients and severe periodontitis was also more frequent among them. Conclusion These findings show the importance of evaluating the periodontal disease and detecting herpesviruses in patients with CKD as the inflammatory process observed in these clinical conditions may worsen the course of both periodontal disease and CKD.